In order to analyze the safety change of an aqueduct in service,the time-discretization method was introduced into the time-varying reliability calculation of the aqueduct structure. Based on a project case, the bearing capacity and crack resistance limit state equation of the rectangular adueduct body were established for three parts in the transverse and longitudinal direction,and the time-varying reliability was calculated. Its accuracy was verified by comparing the calculation results of Monte Carlo method, and compared with the calculation results of dynamic reliability method. The results show that the reliability of the longitudinal bearing capacity of the aqueduct structure decreases with the service life, especially in the later stage of service the decline is much greater than the transverse bearing capacity, indicating that the limit state of the longitudinal bearing capacity is the control state of the aqueduct life. Both the longitudinal and transverse crack resistance reliability decline is slower compared with the bearing capacity reliability. The crack resistance reliability of the bottom plate is slightly lower than the target value in the later stage of service due to the low initial value. The overall calculation error of the time-discretization method is relatively small, especially for the safety evaluation of the structure in the later stage of service. Compared with the dynamic reliability method, the calculation result of the time-discretization method is more accurate. It is more reasonable to use the time-discretization method for the reliability calculation and safety evaluation for aqueducts.